Creating amorphous polymer structure

General Discussion
1

Hi,

I am trying to build an amorphous model of polyurethane and water to simulate diffusion in LAMMPS. I have created a molecule of water and a single polyurethane molecule. How do I create an amorphous model with 100 polyurethane molecules and 50 water molecules. Which is the best way to save the file so that I can import that data file into LAMMPS ?
I need to run the simulation in NPT ensemble, unfortunately its not available in Avagadro. Any suggestions on how to do that ? I am trying to write the input file manually.
Please help.

2

Hi, @Tejas_A. You will need to copy-paste your water and polyurethane to get the needed quantity. Then you can use Auto Optimization Tool (version 1.2 only) to make your system look nicer. I do not work with LAMMPS, but I guess standard .xyz or .pdb formats would work.